Research workbench
Crystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azothiazole-based inhibitor (compound 2)
Analyse Crystal structure of human Casein Kinase I delta in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HMR
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.782
- Source
- Homo sapiens
- Molecule
- Casein kinase I isoform delta
- EC
- 2.7.11.1, 2.7.11.26
- UniProt
- P48730
- Ligands
- GE5
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.782 · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 287 | 40% helix, 18% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 280 | 38% helix, 19% strand | P48730 |
Ligands and binding sites
- GE5 · 3-(2,5-dimethoxyphenyl)-~{N}-[4-[4-(4-fluorophenyl)-2-[(~{E})-phenyldiazenyl]-1,3-thiazol-5-yl]pyridin-2-yl]propanamide · ligand · 2 copies · chains A, B
- MLA · Malonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.63 | 0.83 | 31 | GE5 |
| 2 | 209 | 0.61 | 0.82 | 30 | GE5 |
| 3 | 440 | 0.59 | 0.75 | 38 | empty |
| 4 | 66 | 0.28 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 221 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6HMR · Crystal structure of human casein kinase I delta in complex with a photoswitchable… · the same entry in another collection · chain A against A, TM-score 1.00
- P48730 · AlphaFold monomer V2.0 prediction for casein kinase I isoform delta (P48730) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P48730
- Elsewhere: RCSB PDB 6HMR · PDBe 6HMR · UniProt P48730
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.